[gmx-users] MD simulation on 1 and 4 nodes

[Christoph Freudenberger]

Alexander Zuev wrote:
> Dear all,
> 
> the results of my run with 10 ps MD simulation on 1 and 4 nodes are
> differed from each other:
> 1) from gro-file after mdrun with np=1:
>     2GLU      N   16   1.171   0.770   0.983  0.1916 -0.1159 -0.3137
>     2GLU      H   17   1.143   0.813   0.897 -1.2392 -0.6945 -0.1708
>     2GLU     CA   18   1.226   0.869   1.077 -0.0526 -0.1020 -0.1841
>     2GLU     CB   19   1.234   1.005   1.007  0.3661 -0.2199 -0.3691
>     2GLU     CG   20   1.102   1.058   0.951  0.5377  0.3099 -0.2806
>     2GLU     CD   21   1.089   1.009   0.807  0.7168 -0.5444 -0.0134
>     2GLU    OE1   22   1.016   0.917   0.765 -0.4520  0.5124 -0.3375
>     2GLU    OE2   23   1.158   1.069   0.721  0.1797 -0.1854 -0.1970
>     2GLU      C   24   1.151   0.875   1.210  0.1965 -0.0042 -0.0464
>     2GLU      O   25   1.029   0.880   1.225  0.2254  0.3574  0.0764
> 
> 2) from gro-file after mdrun with np=4:
>     2GLU      N   16   1.141   0.738   0.989  0.1650 -0.2755 -0.3296
>     2GLU      H   17   1.096   0.790   0.917  0.0641  0.4210  0.2319
>     2GLU     CA   18   1.219   0.822   1.081 -0.3070 -0.2080  0.0118
>     2GLU     CB   19   1.273   0.934   0.991 -0.0205  0.1246  0.5967
>     2GLU     CG   20   1.177   1.045   0.949  0.0338 -0.1540 -0.2860
>     2GLU     CD   21   1.068   0.995   0.855 -0.2075  0.6878 -0.4600
>     2GLU    OE1   22   1.106   0.961   0.741  0.0894  0.5117 -0.3091
>     2GLU    OE2   23   0.950   1.003   0.895 -0.0805 -0.3430  0.1321
>     2GLU      C   24   1.150   0.869   1.209 -0.3185 -0.1466 -0.0169
>     2GLU      O   25   1.028   0.880   1.221 -0.3017  0.1736 -0.1484
> 
Do you have several 'GLU' residues in your protein and did you use
-sort -shuffle with grompp for the np4 job?

If so, you might see different 'GLU' residues as resnumber 2 due to
the resorting the molecule for optimal parallel performance.

regards
-- 
Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785